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Cutaneous protothecosis is a rare human infection caused by achlorophyllic algae of the genus Prototheca. It primarily affects immunocompromised individuals, often presenting with nonspecific clinical features that mimic fungal or bacterial infections. Due to its rarity, it is frequently misdiagnosed. We report the case of a 22-year-old immunocompromised male with multiple papules and nodules on the upper and lower limbs and axillae. A clinical diagnosis of fungal infection was initially suspected. Histopathological examination revealed characteristic mulberry-like structures and organisms in a floret arrangement on Periodic-Acid Schiff and Gomori Methenamine Silver stains, leading to a definitive diagnosis of cutaneous protothecosis. The patient responded well to oral itraconazole, with significant clinical improvement. This case highlights the importance of maintaining a high index of suspicion for rare infections like cutaneous protothecosis, particularly in immunocompromised individuals. Early recognition and histopathological confirmation are critical for effective management and favourable outcomes.